2.7 Data availability statement
The newly sequenced mitogenome of O. xuefengensis strain HCMA001 was submitted to GenBank under the accession number SAMN16236787.
3. Results
3.1. Characterization of the four cordyceps mitogenomes
Comparative analysis indicated that the complete mitogenomes of the four cordyceps all comprised circular DNA molecules. The mitogenome length ofO. xuefengensis (78,744 bp) was much smaller than that ofO. sinensis (157,559 bp), but longer than those of Cordyceps militaris (33,277 bp) andC. brongniartii (33,926 bp). All four mitogenomes encoded 14 core PCGs involved in energy metabolism, rps3 involved in translation, and 2 rRNAs. The PCG lengths varied, but the protein coding regions themselves were conserved. The tRNA numbers of the four mitogenomes ranged from 25 (C. brongniartii ) to 27 (O. sinensis ). The tRNAs comprised those for all 20 amino acids and ranged in size from 71 to 86 nucleotides (Table S1). The nucleotide composition of the O. xuefengensis mitogenome was identical to that of O. sinensis , but not to C. militaris and C. brongniartii . The O. sinensis mitogenome had the highest GC content (30.20%), followed by those of O. xuefengensis(29.94%), C. brongniartii (27.34%), and C. militaris(26.79%). The high frequency of A and T usage in codons contributes to the high AT content of the four mitochondrial genomes, with AT content reaching 70.06% in O. xuefengensis , 69.80% in O. sinensis , 73.21% in C. militaris , and 72.66% in C. brongniartii . Both GC skew and AT skew were positive for all four mitogenomes (Table 1).
The O. sinensis mitogenome exhibited an unusually enlarged size (157,559 bp). The compositions of regions were thus analyzed for the mitogenomes, indicating that the protein coding regions among the four mitogenomes are basically identical. A significant difference was observed when comparing intronic and intergenic regions, wherein the total number of intronic nucleotides of the O. sinensis mitogenome was much higher than for those of the other cordyceps, and the total number of intergenic nucleotides of theO. xuefengensis mitogenome is the highest among the four mitogenomes (Fig 2).
The number of introns also significantly differed among the four mitogenomes. Fifty-four introns were present in the mitogenome ofO. sinensis , 18 in that of O. xuefengensis , 8 in that ofC. militaris, and 6 in that of C. brongniartii (Table. 1). Further, the host genes of introns also differ among the four cordyceps. Introns are distributed in the cob (no. of introns: 1),cox1 (1), cox2 (1), cox3 (1), and rnl (4) genes of the C. militaris mitogenome, and in the cob (1),cox1 (2), nad1 (1), and rnl (2) genes of theC. brongniartii mitogenome. In O. xuefengensis , the introns are distributed in cob (2), cox1 (3), cox2(1), cox3 (3), nad1 (2), nad2 (2), nad5 (1),rnl (3), and rns (1) genes, while in the O. sinensis mitogenome, the introns are distributed in the cob (6), cox1 (14),cox2 (6), cox3 (2), nad1 (3), nad2 (2),nad4L (1), nad5 (5), nad6 (1), atp6 (2),atp9 (1), rnl (8), and rns (1) genes (Table S2). The most common intron type among the mitogenomes are group IB introns. Introns also harbor 0–2 homing endonuclease genes, including the LAGLIDADG homing endonuclease and the GIY-YIG endonuclease.
Table 1. Characteristics of cordyceps mitogenomes.